Phases a half-sib family using the block structure and an imputed sire haplotype matrix.

inference

haplotype

reconstruction

phase

Identification of recombination events, haplotype reconstruction, sire imputation and pedigree reconstruction using half-sib family SNP data.

Mohammad Ferdosi

hsphase

Phasing, Pedigree Reconstruction, Sire Imputation and
Recombination Events Identification of Half-sib Families Using
SNP Data

Cedric Gondro

phf function

<dl> <dt>GenotypeMatrix</dt>
<dd><code>matrix</code>. Half-sib genotypes (one half-sib per row; SNPs ordered by mapping position in the columns).
 Data should be numeric: <code>0, 1, 2</code> for <code>AA, AB, BB</code>. Use <code>9</code> for missing data.</dd> <dt>blockMatrix</dt>
<dd><code>matrix</code>. Blocking structure (output of <code>bmh</code>).</dd> <dt>sirePhasedMatrix</dt>
<dd><code>matrix</code>. Imputed sire haplotypes (output of <code>ssp</code>).</dd></dl>

Arguments

Half-sib Family Phasing — phf

<dl>

 <dt>GenotypeMatrix</dt>
<dd><code>matrix</code>. Half-sib genotypes (one half-sib per row; SNPs ordered by mapping position in the columns).
 Data should be numeric: <code>0, 1, 2</code> for <code>AA, AB, BB</code>. Use <code>9</code> for missing data.</dd>

 <dt>blockMatrix</dt>
<dd><code>matrix</code>. Blocking structure (output of <code>bmh</code>).</dd>

 <dt>sirePhasedMatrix</dt>
<dd><code>matrix</code>. Imputed sire haplotypes (output of <code>ssp</code>).</dd>

</dl>

phf: Half-sib Family Phasing

Description

Usage

Value

Arguments

See Also

Examples